The BioMicro Center Supports a number of storage and computational services

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The BioMicro Center has developed and manages a computational infrastructure to support our genomics experimentation and [[BioMicroCenter:BioInformaticsStaff|bioinformatics analysis]]. In response to requests from our users, we have expanded these servers to create a new collaborative computational environment at MIT. These public servers are designed to offer CORE labs access to inexpensive analysis and storage systems that piggy-back on the existing infrastructure. These services are built on a full cost recovery model where the total cost of the servers and services is expected to be recovered over three years. Charges for the equipment are billed on an annual basis.

=== STORAGE ===

=== STORAGE ===

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Large scale data storage is available through the BioMicro Center. Space is available in 1TB increments on an annual basis. The storage is accessible from Window, Macintosh and Linux operating systems and is backed up by MIT's [http://ist.mit.edu/backup/tsm TSM service].<BR><BR>

The BioMicroCenter Public Server (BMC Pub) is a data storage service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible easily from Linux, Windows and Macintosh operating systems. Space is available in 1TB increments. The servers use a RAID6 architecture to accommodate drive failures and are backed up routinely by MIT's [http://ist.mit.edu/backup/tsm TSM] service. Currently the BioMicro Center supports 128TB storage within the BMC-Pub system. More details on how to use the BMC-pub1 system are [[BioMicroCenter:BMCPub|'''found HERE''']]. Pricing for the servers is [[BioMicroCenter:Pricing|on the pricing page.]] Users who would like data storage on the BMC-pub systems should contact [[BioMicroCenter:People|Stephen Goldman]].

For users with appointments in the [http://ki.mit.edu Koch Institute], storage is also available on the KI's Isilon server, Rowley. This Isilon cluster was purchased in September 2010. The server is named after [http://en.wikipedia.org/wiki/Janet_Rowley Janet Rowley], a pioneer in the field of chromosome translocations in cancer and winner of the 2009 national medal of science and 2009 presidential medal of freedom. The cluster currently consists of seven 36NL nodes and three 108NL nodes with a total capacity of over 500TB and is accessible from any networked computer. Rowley serves as the primary storage device used by the BioMicro Center for [[BioMicroCenter:Sequencing|Illumina Sequencing]] and data delivery. Users who would like data storage on Rowley should contact [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

Rous is a Linux cluster, initially purchase in September 2009. Rous, named after the Nobel prize winning cancer researcher [http://www.nobelprize.org/nobel_prizes/medicine/laureates/1966/rous-bio.html Peyton Rous] (and not [http://www.urbandictionary.com/define.php?term=R.O.U.S. Rodents Of Unusual Size]) is equipped with a wide range of bioinformatics software. It uses x86 architecture with 160 processing cores and over 500 GB RAM. Rous is the primary server for handling data analysis from Illumina sequencing and for the GALAXY instance at MIT. Users of Rous '''must''' have an account on either BMC-PUB or on Rowley. <BR><BR>

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Currently, we are reworking the way the queues on Rous work. In addition to a general queue, similar to what is on Rous now, the new system will have lab specific queue where jobs from that lab will have priority on a specific node (or nodes) of the server. Similar to the data storage model, access to these nodes will be on a charge back basis to recover the cost of the instrumentation. We are currently in the testing phase of this project. <BR><BR>

* Currently, users are limited to 24 simultaneous processes on the server.

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* Requests for software changes to Rous should be made to [[BioMicroCenter:People|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

== SOFTWARE ==

== SOFTWARE ==

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===Desktop Software===

===Desktop Software===

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* '''Spotfire Decision Site with Array Explorer for PC''' This highly intuitive database mining software can be used for expression profiling with microarrays and also for a wide range of data analysis .In addition to the basic Spotfire package, we have licensed the array explorer module.

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* [http://biomicro-bioanalyzer.mit.edu/ '''Agilent 2100 Expert'''] This software package is used to control the [[BioMicroCenter:2100BioAnalyzer|Agilent 2100 Bioanalyzer]] and to perform analysis of the output, including microfluidic and electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The software can be installed on your desktop to allow users to do additional analyses.

* [http://biomicro-bioanalyzer.mit.edu/ '''Agilent 2100 Expert'''] This software package is used to control the [[BioMicroCenter:2100BioAnalyzer|Agilent 2100 Bioanalyzer]] and to perform analysis of the output, including microfluidic and electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The software can be installed on your desktop to allow users to do additional analyses.

* [[BioMicroCenter:EVOware|'''Tecan EvoWare Standard''']] This software is available as part of our robotics service. Identical to the software used on the [[BioMicroCenter:Tecan_Freedom_Evo|Tecan EVO 150s]], the software contains a simulator that can be used to design your robotics experiments at your bench.

* [[BioMicroCenter:EVOware|'''Tecan EvoWare Standard''']] This software is available as part of our robotics service. Identical to the software used on the [[BioMicroCenter:Tecan_Freedom_Evo|Tecan EVO 150s]], the software contains a simulator that can be used to design your robotics experiments at your bench.

[http://galaxy.psu.edu/ Galaxy] is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.

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To make things even easier, in collaboration with the [http://luria.mit.edu/CCR_BCC/ Bioinformatics and Computing Core Facility] at the [http://web.mit.edu/ki/index.html Koch Institute]we have created a '''[http://bmc-analyze.mit.edu:8080/ GALAXY INSTANCE]''' here at MIT. This version is still in ALPHA but is available for MIT researchers and it works. Feel free to explore and to begin using it. Some rules:

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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' is for MIT researchers ONLY. Anyone else on the server may have their data deleted at any time -- Just don't do it.

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* File paths, etc, are likely to change.

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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' use will eventually require purchase of storage as part of the BMC-PUB or ROWLEY networks.

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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' runs on the same rous nodes as our Illumina sequencers. Jobs may be deleted if they are abusing the resource.

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These rules are in place for the ALPHA phase and are subject to change without notice. Please email Stuart Levine or Charlie Whittaker with comments and suggestions.

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===Server-Supported Software===

===Server-Supported Software===

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* [http://libguides.mit.edu/content.php?pid=14149&sid=223198 '''GeneGO Metacore'''] GeneGo is a leading provider of data mining & analysis solutions in systems biology. MetaCore, GeneGo's flapship product, is an integrated software suite for functional analysis of experimental data. MetaCore is based on a curated database of human protein-protein, protein-DNA interactions, transcription factors, signaling and metabolic pathways, disease and toxicity, and the effects of bioactive molecules.

* [http://libguides.mit.edu/content.php?pid=14149&sid=223198 '''GeneGO Metacore'''] GeneGo is a leading provider of data mining & analysis solutions in systems biology. MetaCore, GeneGo's flapship product, is an integrated software suite for functional analysis of experimental data. MetaCore is based on a curated database of human protein-protein, protein-DNA interactions, transcription factors, signaling and metabolic pathways, disease and toxicity, and the effects of bioactive molecules.

Other packagesare installed but have not yet been converted to module packages. These include:

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== BIOINFORMATICS SERVICES ==

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* BLAST / BLAT

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* GenePattern

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* IGV

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* MACS

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* MAQ

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* MEME

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* Velvet

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Bioinformatic Services in the BioMicro center are focused primarily on automatic and expanding analyses given to users with their result data. Limitted bioinformatics consulting is also available through [[BioMicroCenter:People|Stuart Levine and Fugen Li]] by appointment for CORE lab members. Bioinformatic projects are undertaken by the BioMicro Center on a '''collaborative''' basis. Expanding the Bioinformatics resources is one of our top priorities. [[BioMicroCenter:Pricing|Prices for Bioinformatics support are available.]]

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== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==

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A critical aspect of providing our users with genomic data is providing our users with the bioinformatics support to interpret their data readily and to assist them in analyzing data for publications and grants. To accomplish this, the BioMicro Center has a team of informatics scientists on staff able to assist labs with experience in a broad number of methodologies. Bioinformatics consultations are available by appointment for MIT scientists affiliated with MIT CEHS or the departments of Biology and Biological Engineering. Bioinformatic projects are undertaken by the BioMicro Center on a ''collaborative'' basis. [[BioMicroCenter:Pricing|Prices for Bioinformatics support are available.]]

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* [[BioMicroCenter:MicroArrayAnalysis|Microarray Analysis]]

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If you are looking for informatics support, the easiest way to begin is with an email to biomicro@mit.edu with a brief description of your experiment. One of the members of our informatics staff will reach out to you to schedule a one on one meeting. This meeting is free for CORE lab members. Once an experimental plan is approved we will begin work on your project, checking in with you at regular intervals to be sure the project is on track. The project can be paused at any time by the researcher.

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* [[BioMicroCenter:IlluminaAnalysis|General Illumina Analysis]]

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* [[BioMicroCenter:ChIPSeqAnalysis|ChIP-seq Analysis]]

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More information about bioinformatics support through the BioMicro Center is available [[BioMicroCenter:BioInformaticsStaff|HERE''']].

* [http://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]

* [http://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]

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== OTHER SERIVCES ==

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===Computing Facilities===

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The BioMicro Center Inforrmation Technology group consists of a full time System Administrator, with subcontracted capabilities in operating and server administration and network implementation. Solutions are tailored to the individual as well as labs needs. System training and documentation is provided and created as needed.

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* '''Security and Network Administration''' The BioMicro Center facility supports a private subnet for improved security and performance. The BioMicro Center employs a Cisco 2641 firewall separating it from the general MIT network. A Cisco 4006 Chassis based switch provides gigabit interfaces from satellite lab switches as well out NET APP fliers and fiber connection to the NE 47 machines room and Beowulf cluster. A local consulting firm assists with security, monitoring and system hardening procedures. These include installing intrusion detection system as well as centrally monitored system “syslog” server which delivers system status every 24 hours by email. The BioMicro Center leverages MIT’s Win Athena network environment which provided tested security patches and well as security based “group policy settings”. All Linux based servers are connected to MIT’s RHEL Satellite update service.

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* '''Data Integrity''' Data generated by the BioMicro Center is stored initially on one of two Net App 880 fiber channel based filers, and are snapped mirrored on a remote tier NETAPP filer over a private network. These three file servers are RAID 10 based and are additionally backed up utilizing MIT’s enterprise level TSM service and are archived in Building W91 on the MIT campus. MIT’s TSM service is also utilized to provide backups for the remaining file servers administered by the BioMicro Center.

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=== OLD INFO ===

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'''Data Storage & Research Network Administration Services'''

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The Department of Biology and Biological Engineering maintain primary network storage of associated labs to facilitate data sharing in the environment surrounding the Biomicro Center. This service is the planned to be phased out due to high support costs.

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Research network support is provided by System Administrator [[BioMicroCenter:People|Stephen]]. Stephen's role is to assist labs by providing network related training, access to the data storage environment, configuring network peripherals, laptops, desktops and independent servers. Information about this storage can be found [[BioMicroCenter:NetworkInformation|HERE]].

HARDWARE

The BioMicro Center has developed and manages a computational infrastructure to support our genomics experimentation and bioinformatics analysis. In response to requests from our users, we have expanded these servers to create a new collaborative computational environment at MIT. These public servers are designed to offer CORE labs access to inexpensive analysis and storage systems that piggy-back on the existing infrastructure. These services are built on a full cost recovery model where the total cost of the servers and services is expected to be recovered over three years. Charges for the equipment are billed on an annual basis.

STORAGE

Large scale data storage is available through the BioMicro Center. Space is available in 1TB increments on an annual basis. The storage is accessible from Window, Macintosh and Linux operating systems and is backed up by MIT's TSM service.

We strongly encourage all labs using Illumina sequencing or bioinformatics analysis to have networked data storage. Either Rowley or BMC-PUB storage is *required* to utilize our computer cluster or our Galaxy server.

The BioMicroCenter Public Server (BMC Pub) is a data storage service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible easily from Linux, Windows and Macintosh operating systems. Space is available in 1TB increments. The servers use a RAID6 architecture to accommodate drive failures and are backed up routinely by MIT's TSM service. Currently the BioMicro Center supports 128TB storage within the BMC-Pub system. More details on how to use the BMC-pub1 system are found HERE. Pricing for the servers is on the pricing page. Users who would like data storage on the BMC-pub systems should contact Stephen Goldman.

For users with appointments in the Koch Institute, storage is also available on the KI's Isilon server, Rowley. This Isilon cluster was purchased in September 2010. The server is named after Janet Rowley, a pioneer in the field of chromosome translocations in cancer and winner of the 2009 national medal of science and 2009 presidential medal of freedom. The cluster currently consists of seven 36NL nodes and three 108NL nodes with a total capacity of over 500TB and is accessible from any networked computer. Rowley serves as the primary storage device used by the BioMicro Center for Illumina Sequencing and data delivery. Users who would like data storage on Rowley should contact Charlie Whittaker.

Rous is a Linux cluster, initially purchase in September 2009. Rous, named after the Nobel prize winning cancer researcher Peyton Rous (and not Rodents Of Unusual Size) is equipped with a wide range of bioinformatics software. It uses x86 architecture with 160 processing cores and over 500 GB RAM. Rous is the primary server for handling data analysis from Illumina sequencing and for the GALAXY instance at MIT. Users of Rous must have an account on either BMC-PUB or on Rowley.

Currently, we are reworking the way the queues on Rous work. In addition to a general queue, similar to what is on Rous now, the new system will have lab specific queue where jobs from that lab will have priority on a specific node (or nodes) of the server. Similar to the data storage model, access to these nodes will be on a charge back basis to recover the cost of the instrumentation. We are currently in the testing phase of this project.

Desktop Software

Agilent 2100 Expert This software package is used to control the Agilent 2100 Bioanalyzer and to perform analysis of the output, including microfluidic and electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The software can be installed on your desktop to allow users to do additional analyses.

Tecan EvoWare Standard This software is available as part of our robotics service. Identical to the software used on the Tecan EVO 150s, the software contains a simulator that can be used to design your robotics experiments at your bench.

Galaxy

Front Page of the MIT Galaxy Site

Galaxy is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.

GALAXY is for MIT researchers ONLY. Anyone else on the server may have their data deleted at any time -- Just don't do it.

File paths, etc, are likely to change.

GALAXY use will eventually require purchase of storage as part of the BMC-PUB or ROWLEY networks.

GALAXY runs on the same rous nodes as our Illumina sequencers. Jobs may be deleted if they are abusing the resource.

These rules are in place for the ALPHA phase and are subject to change without notice. Please email Stuart Levine or Charlie Whittaker with comments and suggestions.

Server-Supported Software

Spotfire is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. The BioMicro Center operates a Spotfire server that is available to anyone at MIT. Licenses for Spotfire are available through the BioMicro Center on a yearly basis.

MATLAB A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.

BioBASE The BIOBASE Knowledge Library (BKL) contains comprehensive sets of protein databases such as HumanPSD, WormPD, GPGR-PD, PombePD, and MycopathPD in addition to analysis tools such as TRANSFAC, TRANSPATH, and ExPlain. BKL brings together curated data, analysis tools, and gene-centered information. BKL is one of the best ways to quickly assess a vast set of protein properties for a given protein or set of proteins.

GeneGO Metacore GeneGo is a leading provider of data mining & analysis solutions in systems biology. MetaCore, GeneGo's flapship product, is an integrated software suite for functional analysis of experimental data. MetaCore is based on a curated database of human protein-protein, protein-DNA interactions, transcription factors, signaling and metabolic pathways, disease and toxicity, and the effects of bioactive molecules.

INGENUITY PATHWAY ANALYSIS software that helps researchers model, analyze, and understand complex biological and chemical systems relevant to their experimental data. Researchers can search the scientific literature and find insights most relevant to their experimental data; analyze and build pathway models related to thier experimental data;and share and collaborate with colleagues. IPA is currently licensed through June 2012.

A critical aspect of providing our users with genomic data is providing our users with the bioinformatics support to interpret their data readily and to assist them in analyzing data for publications and grants. To accomplish this, the BioMicro Center has a team of informatics scientists on staff able to assist labs with experience in a broad number of methodologies. Bioinformatics consultations are available by appointment for MIT scientists affiliated with MIT CEHS or the departments of Biology and Biological Engineering. Bioinformatic projects are undertaken by the BioMicro Center on a collaborative basis. Prices for Bioinformatics support are available.

If you are looking for informatics support, the easiest way to begin is with an email to biomicro@mit.edu with a brief description of your experiment. One of the members of our informatics staff will reach out to you to schedule a one on one meeting. This meeting is free for CORE lab members. Once an experimental plan is approved we will begin work on your project, checking in with you at regular intervals to be sure the project is on track. The project can be paused at any time by the researcher.

More information about bioinformatics support through the BioMicro Center is available HERE.